Candida auris can acquire antifungal resistance without selection pressure

Abstract

The human fungal pathogen Candidozyma auris (formerly Candida auris) can cause prolonged infection outbreaks with high mortality rates in healthcare settings. Treatment failures of patients arise not only from antifungal drug resistance, but also from intra-species variability in pathogenicity as well as induced hypermutation events in response to clinical therapy. Whole genome sequencing was used to identify genetic mutations using the CDC mycoSNPs pipeline. Antifungal susceptibility testing was performed based on Clinical and Laboratory Standards Institute (CLSI) methods. We report here that the interlaboratory exchange of C. auris clinical isolates dried on sterile filter paper, resulted in the emergence of at least three distinct morphotypes following reconstitution. These distinct morphotypes exhibited differences in drug resistance and morphogenesis, linked to the accumulation of mutations in genes associated with azole and echinocandin resistance. Using whole genome sequencing, we identified several variants in TAC1B, MRR1 and FKS2 that correlate with altered drug susceptibilities. Experiments recapitulating filter paper shipment conditions revealed genetic and epigenetic changes, explaining the morphogenetic switching and altered azole resistance. Our findings demonstrate that C. auris can acquire mutations affecting drug resistance traits even in the absence of antifungal exposure, raising concerns about shipment preparation procedures across mycology laboratories. The results are of broad relevance for the medical mycology community, as they call for standardized protocols for exchanging clinical strains, but also experiments to verify phenotypic traits between laboratories. ImportancePathogenesis and antifungal drug resistance traits of Candida auris vary widely across clinical strains and are often attributed to elevated mutation rates. In fungal pathogen research, clinical strains are commonly exchanged between laboratories by transfer on filter paper, a convenient and widely used practice. However, in the case of a C. auris clinical strain received from a collaborating laboratory, we identified multiple acquired mutations. These genetic alterations caused marked changes in morphogenesis and antifungal susceptibility, demonstrating that resistance in C. auris can arise without antifungal selection pressure. Our findings highlight the potential for genetic and phenotypic diversification during routine strain handling and underscore the need for standardized protocols for exchanging clinical C. auris strains across mycology laboratories.